Naruto would punched and killed Nagato then. Only way Nagato would have survived would be due to Konan saving him.If Nagato had remained evil and under his own control especially at his prime I think it's fair to say those two would have ended up the same way and deader than dead the fact remains itachi saved them
Nagato's prime = 6POP
Plus he himself said that Jiraiya was stronger.